A review of current large‐scale mouse knockout efforts

After the successful completion of the human genome project (HGP), biological research in the postgenome era urgently needs an efficient approach for functional analysis of genes. Utilization of knockout mouse models has been powerful for elucidating the function of genes as well as finding new therapeutic interventions for human diseases. Gene trapping and gene targeting are two independent techniques for making knockout mice from embryonic stem (ES) cells. Gene trapping is high‐throughput, random, and sequence‐tagged while gene targeting enables the knockout of specific genes. It has been about 20 years since the first gene targeting and gene trapping mice were generated. In recent years, new tools have emerged for both gene targeting and gene trapping, and organizations have been formed to knock out genes in the mouse genome using either of the two methods. The knockout mouse project (KOMP) and the international gene trap consortium (IGTC) were initiated to create convenient resources for scientific research worldwide and knock out all the mouse genes. Organizers of KOMP regard it as important as the HGP. Gene targeting methods have changed from conventional gene targeting to high‐throughput conditional gene targeting. The combined advantages of trapping and targeting elements are improving the gene trapping spectrum and gene targeting efficiency. As a newly‐developed insertional mutation system, transposons have some advantages over retrovirus in trapping genes. Emergence of the international knockout mouse consortium (IKMP) is the beginning of a global collaboration to systematically knock out all the genes in the mouse genome for functional genomic research. genesis 48:73–85, 2010. © 2010 Wiley‐Liss, Inc.     

The genetic relationship among Iranian ethnic groups: an anthropological view based on HLA class II gene polymorphism

Highly polymorphic human leukocyte antigen (HLA) genes are considered as useful markers by molecular anthropologists to determine genetic relationship among populations. This review summarizes the results of molecular analyses of HLA class II gene polymorphism in 816 DNA samples from 11 Iranian ethnic groups. The genetic relationship of Iranians to Asians and Europeans has also been reported here. The results of this study revealed a close genetic relationship among Iranian subpopulations which were well separated from other Asian and European populations, however, a genetic similarity was observed among Iranians, Macedonians, Greeks, and Italians.     

Subtype Classification of Iranian HIV-1 Sequences Registered in the HIV Databases, 2006-2013

Background

The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the past few years. While the earliest cases were among hemophiliacs, injection drug users (IDUs) fuel the current epidemic. Previous molecular epidemiological analysis found that subtype A was most common among IDUs but more recent studies suggest CRF_35AD may be more prevalent now. To gain a better understanding of the molecular epidemiology of HIV-1 infection in Iran, we analyzed all Iranian HIV sequence data from the Los Alamos National Laboratory.

Methods

All Iranian HIV sequences from subtyping studies with pol, gag, env and full-length HIV-1 genome sequences registered in the HIV databases (www.hiv.lanl.gov) between 2006 and 2013 were downloaded. Phylogenetic trees of each region were constructed using Neighbor-Joining (NJ) and Maximum Parsimony methods.

Results

A total of 475 HIV sequences were analyzed. Overall, 78% of sequences were CRF_35AD. By gene region, CRF_35AD comprised 83% of HIV-1 pol, 62% of env, 78% of gag, and 90% of full-length genome sequences analyzed. There were 240 sequences re-categorized as CRF_AD. The proportion of CRF_35AD sequences categorized by the present study is nearly double the proportion of what had been reported.

Conclusions

Phylogenetic analysis indicates HIV-1 subtype CRF_35AD is the predominant circulating strain in Iran. This result differed from previous studies that reported subtype A as most prevalent in HIV- infected patients but confirmed other studies which reported CRF_35AD as predominant among IDUs. The observed epidemiological connection between HIV strains circulating in Iran and Afghanistan may be due to drug trafficking and/or immigration between the two countries. This finding suggests the possible origins and transmission dynamics of HIV/AIDS within Iran and provides useful information for designing control and intervention strategies.     

Zinc and Copper Levels in Iranian Patients with Psoriasis: A Case Control Study

Zinc and copper are important cofactors and modulators of many critical biological functions in many dermatological diseases including psoriasis. Studies must be performed in different societies to organize a governmental health organization nutritional program. Due to the lack of information related to these trace elements in Iranian psoriasis patients, the aim of this observational case–control study was to compare the serum zinc and copper levels and the zinc/copper ratio in psoriatic patients and healthy volunteers in Northern Iran. Zinc and copper serum concentrations were assayed in 25 selected psoriasis patients and compared with sex- and age-matched healthy volunteers. The mean copper level in psoriatic patients was significantly higher than in healthy volunteers (p?=?0.003), but no significant difference was observed in the zinc concentration between the two groups (p?=?0.57). This study was the first one among Iranian society, and no information have been published in the field yet. The results bring some new information related to Iranian psoriatic patients in contrast to some other studies in different region so that preventive programs could be made in this regard particularly for Iranian population. With respect to the high copper concentration in the Iranian psoriatic population, using copper-chelating agents, such as penicillamine may be suggested for Iranian patients following further comprehensive investigations.     

Oncogenic human papillomavirus genital infection in southern Iranian women: population-based study versus clinic-based data

ABSTRACT: BACKGROUND: Epidemiological studies on genital human papilloma viruses infection (HPVs) in general population are crucial for the implementation of health policy guidelines for developing the strategies to prevent the primary and secondary cervical cancer. In different parts of Iran, there is a lack of population-based studies to determine the prevalence of HPV in the general population. The aim of this population-based study is to compare the prevalence rate of genital HPV infection among reproductive women with our previous clinic-based data, which showed a prevalence rate of 5% in women in southern Iran. RESULTS: Using general primers for all genotypes of HPV, of 799 randomly selected women, five (0.63%, 95% CI 0.23-1.55%) tested positive for HPV DNA. Overall, seven different HPV genotypes were detected: six types (16, 18, 31, 33, 51 and 56) were carcinogenic, or "high risk genotypes" and one genotype (HPV-66) was "probably carcinogenic." CONCLUSIONS: In a population-based study, the prevalence of HPV infection among southern Iranian women was lower than that observed worldwide. However, our gynaecological clinic-based study on the prevalence of HPV infection showed results comparable with other studies in the Middle East and Persian Gulf countries. Since gynaecological clinic-based data may generally overestimate HPV prevalence, estimates of prevalence according to clinic-based data should be adjusted downward by the population-based survey estimates.     

Diversity in palmar pattern ridge counts among 12 Iranian populations

Bilateral palmar prints of 604 male individuals from 12 Iranian groups, six Mongoloid and six Caucasoid, have been analyzed for palmar pattern ridge counts (PPRC). Highly significant variation has been observed in the size of the palmar patterns in all the configurational areas among the Iranian groups. The distance analysis based on PPRCs differentiated the Iranian Mongoloid from the Iranian Caucasoid groups into distinct clusters. The pattern of differentiation based on PPRCs explained the ethnohistoric relationships between the Iranian groups as well as between the Iranian and the 20 Caucasoid groups from India much better than the palmar pattern frequencies. The results of this study demonstrate the existence of variation in the size of the palmar patterns across different populations within an ethnic group, as well as that among different ethnic groups, and seems to be a better indicator of interpopulational diversity than the palmar pattern frequencies.     

Serum zinc levels and goiter in Iranian school children

Iodine deficiency has been shown to have high prevalence in Iran despite sufficient iodine supplementation. Zinc deficiency may also contribute to the pathogenesis of endemic goiter. The aim of this study was to compare serum zinc level in Iranian school children with and without goiter. A cross-sectional study was performed among urban children aged 8-12 years in city of Kerman, Iran. A multistage proportional to size cluster sampling method was used to screen 5500 subjects out of 29,787 students. After the screening phase, serum and urine specimens of randomly selected 165 students were evaluated for serum zinc levels and urinary iodine excretion and compared in goiterous and non-goiterous children. Serum zinc level was 149.5±29.4 μg/l in goiterous children and 141.2±52 μg/l in non-goiterous children but no significant difference was found between the groups (p=0.37). But urinary iodine excretion was significantly (p<0.001) lower in goiterous children (207.5 μg/l in goiterous children and 262.5 μg/l in non-goiterous children). This study showed that serum zinc level in goiterous and non-goiterus children is not different and zinc deficiency is not a risk factor for endemic goiter in this population.     

Assessment of patrilineal gene pool of the Iranian Azeris

The Iranian Azeris are the largest ethno-linguistic minority in Iran who live mainly in the north-west part of the country. Located in the crossroad of ancient human migrations the Iranian Azeris bear the complicated historical influence of the region in their gene pool. Despite the importance of Iranian Azeris in reconstructing the historical event of the Middle-East, their (genetic) origin still remains heavily disputed. In this study we tried to evaluate the rates of genetic contribution of possible source populations (namely, indigenous Iranian, Caucasian, and Central Asian) in the gene pool of modem Iranian Azeris through paternally inherited Y-chromosomal 6 STR markers. The assessment of genetic distances reveals that the Iranian Azeris are mixed population with substantial North Caucasian genetic contribution being genetically much closer to their immediate neighboring ethnic groups. Based on the results of admixture analysis we can conclude that there are significant Caucasian and no visible Central Asian contribution to the gene pool of modern Iranian Azeris.     

Assessment of salinity indices to identify Iranian wheat varieties using an artificial neural network

In arid and semi‐arid regions of the world, including Iran, soil salinity is one of the major abiotic stresses. One of the ways to achieve high performance in these areas is to use salt‐tolerant varieties of wheat. Iran is known as one of the places where the D‐genome originated and evolved. In order to evaluate the salt tolerance of Iranian genotypes based on the eight indices using analysis of variance, regression and an artificial neural network (ANN), 41 Iranian wheat varieties (Trticum aestivum L.) were planted in a randomised complete block design with three replications under two saline irrigation conditions, 0.631 and 11.8 dS m^?1, in Kerman, Iran. Significant differences between the varieties were observed, and the significant two‐way interaction of environment × varieties in combined analysis and non‐significant correlation, 0.07, between the yield in two environments (yield in non‐stress conditions, Yp, and yield in stress conditions, Ys) indicates the existence of genetic variation among varieties and the different responses of the varieties in both the environments. The indices of tolerance, geometric mean product (GMP), mean product (MP), harmonic mean (HM) and stress tolerance index (STI) were calculated based on grain yield evidence of positive significant correlation with Yp and Ys. Based on the ANN results, yield stability index (YSI), MP, GMP and STI were the best indices to predict salinity‐tolerant varieties. The varieties selected based on these indices, such as Bolani, Sistan, Ofogh, Pishtaz, Karchia and Arg, produced high yield in both the environments. These results show that bread wheat originating from Iran has salt tolerance potential and can also be used in studies related to salinity tolerance mechanisms.     

Genotypic characterization of Iranian camel (Camelus dromedarius) isolates of Echinoccocus granulosus

In the present study, Echinoccocus granulosus isolates collected from camels (Camelus dromedarius) in eastern Iran were characterized based on the nucleotide sequences of mitochondrial CO1 and NDI genes. The molecular results for camel isolates demonstrated that at least 2 different genotypes are present, i.e., a buffalo genotype (G3) and the camel genotype (G6). Although the sequences of the Iranian camel genotype (G6) are completely homologous to the reference sequence of G6 (M84666) of E. granulosus , a nucleotide mutation (C to T at position 168) was detected in the CO1 sequences of the Iranian G3 isolates (HM626405) when compared with the reference G3 genotype (M84663). The findings of the present study represent the demonstration of the buffalo strain in camels. As previously reported, humans can be infected by this genotype; accordingly, the epidemiological importance of this genotype in the camel population should be considered in further studies.     

The Bermuda Triangle: The Pragmatics,Policies, and Principles for Data Sharing in the History of the Human Genome Project

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.     

Mitochondrial DNA D‐loop sequence variation in maternal lineages of Iranian native horses

To understand the origin and genetic diversity of Iranian native horses, mitochondrial DNA (mtDNA) D‐loop sequences were generated for 95 horses from five breeds sampled in eight geographical locations in Iran. Sequence analysis of a 247‐bp segment revealed a total of 27 haplotypes with 38 polymorphic sites. Twelve of 19 mtDNA haplogroups were identified in the samples. The most common haplotypes were found within haplogroup X2. Within‐population haplotype and nucleotide diversities of the five breeds ranged from 0.838 ± 0.056 to 0.974 ± 0.022 and 0.011 ± 0.002 to 0.021 ± 0.001 respectively, indicating a relatively high genetic diversity in Iranian horses. The identification of several ancient sequences common between the breeds suggests that the lineage of the majority of Iranian horse breeds is old and obviously originated from a vast number of mares. We found in all native Iranian horse breeds lineages of the haplogroups D and K, which is concordant with the previous findings of Asian origins of these haplogroups. The presence of haplotypes E and K in our study also is consistent with a geographical west–east direction of increasing frequency of these haplotypes and a genetic fusion in Iranian horse breeds.     

Current trends in mapping human genes

The human is estimated to have at least 50,000 expressed genes (gene loci). Some information is available concerning about 5000 of these gene loci and about 1900 have been mapped, i.e., assigned to specific chromosomes (and in most instances particular chromosome regions). Progress has been achieved by a combination of physical mapping (e.g., study of somatic cell hybrids and chromosomal in situ hybridization) and genetic mapping (e.g., genetic linkage studies). New methods for both physical and genetic mapping are expanding the armamentarium. The usefulness of the mapping information is already evident; the spin-off from the Human Genome Project (HGP) begins immediately. The complete nucleotide sequence is the ultimate map of the human genome. Sequencing, although already under way for limited segments of the genome, will await further progress in gene mapping, and in particular creation of contig maps for each chromosome. Meanwhile the technology of sequencing and sequence information handling will be developed. It is argued that the HGP is a new form of coordinated, interdisciplinary science; that its primary objective must be seen as the creation of a tool for biomedical research--a source book that will be the basis of study of variation and function for a long time; that the impact on scientist training will be salutary by relieving graduate students of useless drudgery and by training scientists competent in both molecular genetics and computational science; and that the funding of the HGP will have an insignificant negative effect on science funding generally, and indeed may have a beneficial effect through economy of scale and a focusing of attention on the excitement of biology and medical science.     

Diversity of Sinorhizobium strains nodulating Medicago sativa from different Iranian regions

Alfalfa is believed to have originated in north-western Iran and has a long history of coexistence with its bacterial symbiont Sinorhizobium in soils of Iran. However, little is known about the diversity of Sinorhizobium strains nodulating Iranian alfalfa genotypes. In this study, Sinorhizobium populations were sampled from eight different Iranian sites using three cultivars of Medicago sativa as trap host plants. A total of 982 rhizobial strains were isolated and species were identified showing a large prevalence of Sinorhizobium meliloti over Sinorhizobium medicae. Analysis of salt tolerance demonstrated a great phenotypic diversity. The genetic diversity of the Sinorhizobium isolates was analysed using BOX-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR. Patterns ofBOX-PCR fingerprinting were statistically analysed with AMOVA to evaluate the role of plant variety and site of origin in the genetic variance observed. Results indicated that most of the total molecular variance was attributable to divergence among strains isolated from different sites and cultivars (intrapopulation, strain-by-strain variance). Moreover, the analysis showed the presence of two geographic populations (west and northwest), indicating that the effect of the site of origin could be more relevant in shaping population genetic diversity than the effect of cultivar or individual plant.     

Identifying biodiversity hotspots for threatened mammal species in Iran

Conservation biology has much more attention for biodiversity hot spots than before. In order to recognize the hotspots for Iranian terrestrial mammal species that are listed in any red list, nationally or globally, ten Species Distribution Models (SDMs) have been applied. The SDMs evaluation results based on the TSS and AUC values showed that all ten models of habitat suitability perform significantly better than the random selection for all studied species. According to the results, biodiversity hotspots for threatened mammal species are located in north, west and central of Iran, along the Zagros and Alborz mountain range. Therefore, habitats for threatened mammal species have been limited to small parts of Iran (approximately 27% of the country). These areas are severely fragmented and only 57% of them have been announced protected by the current conservation system. The suggestion is that, as the sustainability of these habitats would strongly depend on maintaining dispersal corridors to facilitate the movement of animals among the habitat fragments, conservation efforts should focus on those hotspots which are not formally protected under conservation laws.     

Annotated checklist of Iranian Hydrophilidae (Coleoptera: Polyphaga: Hydrophiloidea)

This checklist comprises all species of Hydrophilidae (Coleoptera: Hydrophiloidea) quoted in the literature referring to Iran and confirmed by our study. In total, 104 species within 17 genera and five subfamilies, Hydrophilinae (eight genera, 63 species), Chaetarthriinae (three genera, five species), Enochrinae (single genus, 20 species), Acidocerinae (single genus, three species) and Sphaeridiinae (four genera, 13 species), are listed for the fauna of Iran. Three species are endemic; four species are recorded here for the first time from Iran, and nine species are excluded from Iranian fauna.     

Cancer incidence in Iran in 2014: Results of the Iranian National Population-based Cancer Registry

BackgroundWe aimed to report, for the first time, the results of the Iranian National Population-based Cancer Registry (INPCR) for the year 2014.MethodsTotal population of Iran in 2014 was 76,639,000. The INPCR covered 30 out of 31 provinces (98% of total population). It registered only cases diagnosed with malignant new primary tumors. The main sources for data collection included pathology center, hospitals as well as death registries. Quality assessment and analysis of data were performed by CanReg-5 software. Age standardized incidence rates (ASR) (per 100,000) were reported at national and subnational levels.ResultsOverall, 112,131 new cancer cases were registered in INPCR in 2014, of which 60,469 (53.9%) were male. The diagnosis of cancer was made by microscopic confirmation in 76,568 cases (68.28%). The ASRs of all cancers were 177.44 and 141.18 in male and female, respectively. Cancers of the stomach (ASR = 21.24), prostate (18.41) and colorectum (16.57) were the most common cancers in men and the top three cancers in women were malignancies of breast (34.53), colorectum (11.86) and stomach (9.44). The ASR of cervix uteri cancer in women was 1.78. Our findings suggested high incidence of cancers of the esophagus, stomach and lung in North/ North West of Iran.ConclusionOur results showed that Iran is a medium-risk area for incidence of cancers. We found differences in the most common cancers in Iran comparing to those reported for the World. Our results also suggested geographical diversities in incidence rates of cancers in different subdivisions of Iran.     

First report of computational protein–ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients

BackgroundIran has recently included integrase (INT) inhibitors (INTIs) in the first‐line treatment regimen in human immunodeficiency virus (HIV)-infected patients. However, there is no bioinformatics data to elaborate the impact of resistance-associated mutations (RAMs) and naturally occurring polymorphisms (NOPs) on INTIs treatment outcome in Iranian patients.MethodIn this cross-sectional survey, 850 HIV-1-infected patients enrolled; of them, 78 samples had successful sequencing results for INT gene. Several analyses were performed including docking screening, genotypic resistance, secondary/tertiary structures, post-translational modification (PTM), immune epitopes, etc.ResultThe average docking energy (E value) of different samples with elvitegravir (EVG) and raltegravir (RAL) was more than other INTIs. Phylogenetic tree analysis and Stanford HIV Subtyping program revealed HIV-1 CRF35-AD was the predominant subtype (94.9%) in our cases; in any event, online subtyping tools confirmed A1 as the most frequent subtype. For the first time, CRF-01B and BF were identified as new subtypes in Iran. Decreased CD4 count was associated with several factors: poor or unstable adherence, naïve treatment, and drug user status.ConclusionAs the first bioinformatic report on HIV-integrase from Iran, this study indicates that EVG and RAL are the optimal INTIs in first-line antiretroviral therapy (ART) in Iranian patients. Some conserved motifs and specific amino acids in INT-protein binding sites have characterized that mutation(s) in them may disrupt INT-drugs interaction and cause a significant loss in susceptibility to INTIs. Good adherence, treatment of naïve patients, and monitoring injection drug users are fundamental factors to control HIV infection in Iran effectively.     

Genomics: shifts in metaphorical landscape between 2000 and 2003

This article examines the shifts and changes in the metaphors used to describe the human genome and the human genome project (HGP) between 2000 and 2003, with the year 2001 as a trigger for genomic and metaphorical reflection. We want to answer questions, such as: Did the findings announced in 2001 shake the metaphorical foundations on which the HGP had been built or not? Did novel metaphors capture the imagination of scientists and the public or did old metaphors survive throughout this period? What influence does the continuity or discontinuity in metaphorical framing of the HGP have on the public perception of the HGP as well as on its scientific understanding? To answer these questions we have systematically compared the metaphors used in one major scientific journal, Nature, and in one major UK newspaper, the online edition of the Guardian/The Observer during a period of two months around June 2000, February 2001 and April 2003.     

Molecular phylogeny and intraspecific differentiation of the Eremias velox complex of the Iranian Plateau and Central Asia (Sauria,Lacertidae)

The Central Asian racerunner, Eremias velox, is a widely distributed lizard of the Eurasian lacertid genus Eremias. Nucleotide sequences of mitochondrial genes, cyt b and 12S rDNA from 13 geographically distant localities in Iran and Central Asia, were analysed. Phylogenetic analyses of the sequence data unambiguously recovered five major clades within the E. velox complex with a high level of genetic divergence, indicating long periods of isolation. The basal position of the Iranian clades in the phylogenetic trees suggests that the E. velox clade originated on the Iranian plateau in the Middle Miocene. According to our calibrations, the northern Iranian clade diverged first some 10–11 Ma and that the Central Asian lineages split from the northeastern Iranian lineage approximately 6 Ma, most likely as a result of uplifting of the Kopet‐Dagh Mountains in the northern margin of the Iranian plateau. Topology of the phylogenetic trees, combined with the degree of the genetic distances among the independent lineages recovered in this study, provide a solid foundation for a fundamental revision of the taxonomic status of the major clades within this species complex.